Chapter 3 : Creating and Analyzing a Project
Contents
1. Once you make your selection click the Add button These samples will now appear in the sample management table in the Data tab Figure 3 6 Selecting samples from other projects showing two files selected Create a new blank sample Samples can be added one at a time by selecting the Create a new blank sample option Figure 3 7 In the following dialog box type a sample name and click Chapter 3 Creating and Analyzing a Project 7 Create This process creates a sample entry in the sample management table but there is no associated file with it hence it is a blank sample Expanding the sample management table by clicking the expand triangle icon on the right side of the table will reveal the option to associate files to the blank sample Mouse over the column and click the green icon to associate a file s to the sample Perform the process for every sample in your project Figure 3 7 Adding a blank sample Adding samples using a Plugin Samples can also be created by Partek plugins that uploads data from other analysis software into the Partek Flow server One example is the PartekFlowUploader which runs within the Torrent Suite Software of Ion Chapter 3 Creating and Analyzing a Project 8 Torrent machines The plugin can be run manually after the data has been collected or it can be included in the run plan Data is uploaded to a specified Partek Flow server and samples are added to a project bas2. File names or Sample names will be chosen during the process The last column cannot have empty values the table cannot be ragged Missing data blank cells can only be handled if the attribute is numeric If it is categorical please put a character in it Using Sample name as the unique identifier in the first column makes more sense when Samples are associated with more than one file for instance paired end reads and or technical replicates If file names are used to assign attributes and a sample is associated with more than one file assigned attributes will be based on the first file on the list that matches a filename associated with that sample The files were imported in the SRA format from the Sequence Read Archive database In Partek Flow they are automatically converted to the FASTQ format Consequently their filenames would change once they are imported The new file names can be seen by expanding the sample management table Figure 3 5 the new extension would be fastq gz If attributes are assigned from a file to the same project twice two things may happen If the previous attributes have the same header and type both are either categorical or numeric the values are overwritten If there are different additional headers on the second round of assignment these new attributes will show up For numeric attributes a blank value can t override a previous value
3. Running Done Canceled If the task is currently running a status progress bar will appear in the column Once completed the status of a task will be Done and the End column will be updated with the completion time A waiting task is may be waiting for upstream tasks to complete or waiting for more computing resources to be available The Action column contains the cancel button that if clicked will allow canceling of the task Both pending tasks and running tasks can be cancelled A trash icon will appear in the Action column for completed canceled or failed tasks and will allow the task to be deleted from the project Deleting a task in the Queue tab will remove the corresponding nodes in the Analyses tab Unless the user has admin privileges a user may only cancel and delete a task that he she started The User End and Status columns may be used to filter the table Chapter 3 Creating and Analyzing a Project 34 3 6 The Collaborators Tab The Collaborators tab provides an overview of users associated with a particular project and enables project creators and administrators to add collaborators Figure 3 36 A user without administrator status has to be specified as a collaborator in a project to be able to access the project in his her home folder and to perform tasks To add a collaborator type a username in the Add a collaborator box and click the button Previous collaborators may be selected usi
4. in the next section Figure 3 27 Warnings indicate that the task failed or was cancelled and the data node is empty the example shows failure of the subsampling task and as a consequence an empty Subsampled reads node To delete tasks from the project click the right mouse button on the task node and then select Cancel Figure 3 28 Alternatively select the task node click Delete task from the task pane The nodes downstream of this task will be deleted However deleting the output files is optional Figure 3 28 inset Chapter 3 Creating and Analyzing a Project 27 Figure 3 28 A task can be deleted by right clicking on the task or selecting Delete task in the task panel Deleting the task s output files is optional inset In addition to using the right mouse button and the task pane tasks can also be deleted and cancelled in the Queue tab see section 3 5 Chapter 3 Creating and Analyzing a Project 28 3 4 4 Task Results and Task Actions Selecting a task node will reveal a task pane with two sections Task results and Task actions Figure 3 29 Figure 3 29 A task pane showing a menu for a task node different tasks will show different options an example is shown Items from the Task results section inform on the action performed in that node Certain tasks generate a Task report Figure 3 30 which include any tables or charts that the task may have produced Figure 3 30 An example of a Task report A Quantif
5. 3 alignment was performed on the unaligned reads Two additional nodes were added a task node for Align reads and an output data node containing the Aligned reads Figure 3 23 Certain tasks performed on a data node generate additional data nodes The example shows the Aligned read nodes which was generated upon alignment of the Unaligned reads node Chapter 3 Creating and Analyzing a Project 24 3 4 3 Running a task To run a task select a data node and then locate the task you wish to perform from the task pane Mouse over to see a description of the action to be performed Figure 3 24 Click the specific task set the additional parameters and click Finish The task will be scheduled the display will refresh and the screen will return to the project s Analyses tab In Figure 3 24 the aligner Bowtie 2 was selected and the choices for the aligner index and additional alignment options appeared Figure 3 24 Running a task in the Analyses tab of Partek Flow Dialog boxes to set the parameters appear the example shown on insets is alignment of unaligned reads Tasks that are currently running or scheduled in the queue appear in a lighter shade of blue The progress of the task is indicated by the darkening of the color blue within the task node from left to right Hovering the mouse pointer over the node will highlight the related nodes with a thin black outline and display the status of the task Figure 3 25 If a task is ex
6. Chapter 3 Creating and Analyzing a Project 1 Chapter 3 Creating and Analyzing a Project Partek Flow software manages experiments as projects A complete project consists of input data tasks used to analyze the data the resulting output files and a list of users involved in the analysis This chapter provides instructions in creating and analyzing a project and covers Types of data Creating a new project The data tab The analyses tab The queue tab The collaborator tab Project management 3 1 Types of Data Partek Flow can import both unaligned and aligned NGS data The following file types are valid and will be recognized by the Partek Flow file browser fasta bam fastq sam sff sra csfasta csfastq qual gz There is no need to unzip compressed gz files In cases where there is paired end data files will also be automatically recognized and their paired relationship will be maintained throughout the analysis Matching on paired end files is based on file names every character in both file names must match except for the section that determines whether a file is the first or the second file For instance if the first file contains _R1 _1 _F3 _F5 in the file name the second file must contain something in the lines with the following _R2 _2 _F5 _F5 P2 _F5 BC _R3 _R5 etc The identifying section must be s
7. Deleting or Renaming samples within a Project In the Data tab each sample can be renamed or deleted from the project by clicking the gear icon next to the sample name The gear icon is readily visible upon mouse over Deleting a sample from a project does not delete the associated files which will remain on the disk Chapter 3 Creating and Analyzing a Project 20 Figure 3 18 Renaming or deleting a sample an example is shown Chapter 3 Creating and Analyzing a Project 21 3 4 The Analyses Tab After samples have been added and associated with valid data files a data node will appear in the Analysis tab Figure 3 19 The Analyses tab is where different analysis tools and the corresponding reports are accessed Figure 3 19 The Analyses tab showing a data node of unaligned reads an example is shown 3 4 1 Data and Task nodes The Analyses tab contains two elements data nodes circles and task nodes rounded rectangles connected by lines and arrows Collectively they represent a data analysis pipeline Customized pipelines can be pre built or created and is the subject of Chapter 13 Data nodes Figure 3 20 may represent a file imported into the project or a file generated by Partek Flow as an output of a task e g alignment of FASTQ files generates BAM files Chapter 3 Creating and Analyzing a Project 22 Figure 3 20 Examples of different types of data nodes Task nodes Figure 3 21 represent the analysis steps p
8. Figure 3 32 Adding a task description The dialog box is shown as well as the displayed description upon mouse over highlighted an example is shown 3 4 5 Layers It is common within next generation sequencing data analysis to explore different settings of tasks for comparison and optimization Users may modify an upstream step for example the alignment parameters and inspect the downstream effect on the results such as percent aligned reads The implementation of Layers in Partek Flow makes this easy and organized Instead of creating separate nodes in a pipeline another set of nodes with a different color is stacked behind ones that have been repeated Figure 3 33 To see the parameters that were changed between runs hover the mouse icon over the set of stacked task nodes and a pop up balloon will display them with the color of the letters matching the color of each layer Chapter 3 Creating and Analyzing a Project 31 Figure 3 33 Analysis showing layers The same task was repeated with different parameters Hovering the mouse pointer over the layers shows the parameters that were changed In the example shown in the figure the quantification in the blue layer was performed with require_proper_pair argument set to false while the quantification in the green layer was performed with the require_proper_pair argument set to true Layers are formed when the same task is performed on the same data node more than once They are also
9. The Queue Tab The Queue tab contains a table of the tasks that are running scheduled or completed in the Partek Flow project Figure 3 35 It provides an overview of the task progress enables task management and links to detailed reports for each task Figure 3 35 The Queue tab showing running waiting and done tasks an example is shown Chapter 3 Creating and Analyzing a Project 33 Each row of the table corresponds to a task node in the Analyses tab The list can be sorted according to a specific column using the sort icon The Task column lists the name of the tasks On the left of the task name is a colored circle indicating the layer of this task The column is searchable by task name Clicking the task name will open the Task report page If the task did not generate a report the link will go to the Task details page The User column identifies the task owner Aside from the user who created the project only collaborators and users with admin privileges can start tasks in a project See section 3 6 of this chapter for further information Clicking a name in the User column will display the corresponding User profile The End column shows the task completion time It will show the actual time for completed tasks and the estimated time for running tasks These estimates improve in accuracy as more tasks are completed in the current Partek Flow instance The Status column displays the current status of the task such as Waiting
10. adio buttons next to Attributes in file refer to The headers of the text file will be recognized and options for their import will appear Imported attributes that do not currently exist in the project will create new project specific attributes Each header of the table would be an attribute and the user has the option to change the name Columns containing letter characters are automatically selected as categorical attributes Columns containing numbers are suggested to be numeric attributes and can be changed to categorical using the drop down menu under Attribute type Unclicking the check mark would skip this column and ignore the attribute To proceed click Import The following are guidelines for preparing the sample annotation text file The first column is always the unique identifier and can refer only to File names or Sample names Chapter 3 Creating and Analyzing a Project 19 If using Sample names in the first column they must match the entries of the Sample name column in the sample management table If using File names in the first column use the filenames shown in the fastq column of the expanded sample management table Figure 3 5 then add the extension gz All filenames must include the complete file extension e g Samplename fastq gz The header name of the first column of the table top left cell of our text table is irrelevant but should not be left blank Whether the first column contains
11. e management table Chapter 3 Creating and Analyzing a Project 13 Figure 3 12 Adding a numeric attribute and specifying the units All numeric attributes automatically have system wide visibility Adding a system wide attribute System wide attributes include numeric attributes created by other users as well as categorical attributes defined by admins Since they do not have to be created by the current user they only need to be added to the sample management table in a project In the Data tab click Add a system wide attribute button Figure 3 13 In the dialog box that follows a drop down menu is located next to Add attribute where you can select the System wide attribute you would like to add to the project Once selected it will be recognized automatically as either Categorical system wide or the Numeric attribute For an System wide categorical attribute the different categories are listed and you have the option of pre filling the columns with N A or any other category within the attribute Click Add column and you will return to the Data Tab Chapter 3 Creating and Analyzing a Project 14 Figure 3 13 Adding a system wide categorical attribute column Assigning categories or values to attributes After adding all the desired attributes to a project the sample management table will show a new column for each attribute Figure 3 14 The columns will initially appear blank as the samples have not yet been categorized or as
12. ed on their filenames For more information on the PartekFlowUploader please see the appropriate literature from Ion Torrent Adding Files to an existing project Additional samples can be added to an existing project simply by opening the project going to the Data tab and clicking the Add samples button Figure 3 8 The three Add samples options will be revealed Figure 3 8 The Add samples button in the Partek Flow Data tab red arrow will reveal options for adding samples inset An example of the project output directory is highlighted 3 3 2 Project output directory The project output directory is the folder in the Partek Flow server where all the files produced during analysis will be stored Chapter 3 Creating and Analyzing a Project 9 The default directory is configured by the Partek Flow Administrator under the Settings menu under System Preferences gt Default project output directory For additional details see the System settings section of Chapter 14 If the user does not override the default the task output will go to a subdirectory with the name of the Project An example is shown in Figure 3 8 inset The user has the option of specifying an existing folder or creating a new one as the project output directory To do so click the Change link and specify or create a new folder in the dialog box 3 3 3 Sample Annotation After samples have been added in the project additional information about the
13. eparated from the rest of the file name with underscores or dots If two conflicting identifiers are present then the file is treated as single end For example s_1_1 matches s_1_2 as described above However s_2_1 does not mate with s_1_2 and the files will be treated as two single end files Chapter 3 Creating and Analyzing a Project 2 3 2 Creating a New Project Using a web browser log in to Partek Flow From the Home page click the New Project button enter a project name Figure 3 1 and then click Create project Figure 3 1 Partek Flow Home page and the dialog box for naming a project inset The Project name is the basis of the default name of the output directory for this project Project names are unique thus a new project cannot have the same name as an existing project within the same Partek Flow server Once a new project has been created the user is automatically directed to the Data tab of the Project View Chapter 3 Creating and Analyzing a Project 3 3 3 The Data Tab The Data Tab is where users can add samples import data and assign sample attributes This is also where users can modify the location of the project output folder 3 3 1 Adding samples For a new project where no samples have yet been added the Data tab will appear as in Figure 3 2 To add samples to the project click Add samples Three options will be displayed Figure 3 2 inset Figure 3 2 Partek Flow Data tab and the options fo
14. erformed on the data within a project For details on the tasks available in Partek Flow see the specific chapters of this user manual dedicated to the different tasks Figure 3 21 Examples of different types of task nodes 3 4 2 The Task Pane Clicking on a node reveals the task pane Figure 3 22 a data specific menu on the right side of the screen Figure 3 22 The task pane red box is revealed when a node is selected A feature of Partek Flow software is that only the tasks that are available for the selected node will be listed in the task pane For data nodes actions that can be performed on that specific data type will appear A bold black line around a node Click a data node to reveal the task pane Chapter 3 Creating and Analyzing a Project 23 indicates that it is selected During analysis only one node can be selected at a time In Figure 3 22 a node that contains Unaligned reads is selected The tasks listed are the ones that can be performed on unaligned data QA QC Pre analysis tools and Aligners To hide the task pane simply click the symbol on the upper left corner of the task pane Clicking the triangles will collapse or expand the different groups of tasks that are shown After a task is performed on a data node a new task node is created and connected to the original data node Depending on the task a new data node may automatically be generated that contains the resulting data In Figure 3 2
15. fied In the expanded view mouse over the column of a sample The highlighted icons will correspond to the options for the sample on that row Click the green icon to associate additional files or the red icon to dissociate a file from a sample You can manually associate multiple files with Chapter 3 Creating and Analyzing a Project 6 one sample Dissociating a file from a sample does not delete the file from the Partek Flow server Import samples from another project This method adds samples from previously created projects within the same Partek Flow server to a new project This option is useful for re analyzing a dataset in a new project analyzing a subset of a data from a previous project or combining data from different projects Select the Import samples from another project button A dialog box will allow selection of the samples Figure 3 6 The dropdown menu of Project lists the existing projects that the current user has access to They may be previous projects from the same user previous projects from collaborators or if the user has an administrative account all the projects in the Partek Flow server Click the Project dropdown menu to select an existing project In the Samples box you will find a list of samples from the selected project Choose the samples you wish to add to your new project by highlighting them using your mouse If needed use the keyboard Ctrl or Shift key to select more than one sample
16. formed when a task node is selected and the Re run it w new parameters is selected in the task pane Figure 3 29 This will allow the users to change the options only for the selected task The user may choose to re run the task to which the changes have been made as well as all the downstream tasks until the analysis is completed To do so select Re run w new parameters downstream tasks from the task pane With layers only a single task is changed at a time although several settings of the task can be altered The options of all the downstream tasks will remain the same To select a different layer use the left mouse button to click on any node of the desired layer All the nodes associated with the selected layer have the same color and will be displayed on the top of the stack 3 4 6 Downloading your Data Data associated with any data node can be downloaded using the Download data link in the task pane Figure 3 34 Compressed files will be downloaded to the local computer where the user is accessing the Partek Flow server Note that bigger files such as unaligned reads would take longer to download For guidance a file size estimate is provided for each data node These zipped files can easily be imported by the Partek Genomics Suite software and is the subject of Chapter 15 Chapter 3 Creating and Analyzing a Project 32 Figure 3 34 Downloading the data from a data node using the task pane an example is shown 3 5
17. hapter 14 for more information A feature of Partek Flow is the use of controlled vocabulary for categorical attributes allowing samples to be assigned only within pre defined categories It was designed to effectively manage content and data and allow teams to share common definitions The use of standard terms avoids misunderstanding and unnecessary renaming tasks in the later stages of analysis Chapter 3 Creating and Analyzing a Project 11 To add a categorical attribute in the Manage attributes page click the Add new attribute Figure 3 10 In the dialog box type a Name for the attribute select the Categorical radio button next to Attribute type and then click the Add button Figure 3 10 Adding a categorical attribute and defining the categories Individual categories for the attribute must then be entered Enter a name of the New category and click Add The Name of the new category will show up in the table Figure 3 10 lower right inset The category can also be edited by clicking or deleted by clicking Additionally sub categories can be added by clicking in the Options column After all the categories have been added to this attribute click Close to proceed Repeat the process for additional attributes of the samples in your study When done click Back to sample management table Categorical attributes will default to Project specific visibility Admin accounts have additional option of making the new attribute visible Sy
18. ng a text editor prepare a table containing the attributes An example is shown in Figure 3 16 There should only be one tab between columns with no extra tabs after the last column In this particular example the first column contains the filename and the text file is saved as Sampleinfo txt Figure 3 16 A sample annotation text file This view has the non printing characters visible to show the tab stops Appearance will vary depending on the text editor used The first row of the table in the text file contains the attributes as headers The first column of the table in the text file regardless of the header of the first column should contain either the sample names or the file names of the samples already added in Partek Flow The first column is the unique identifier that will match the samples to the correct values or categories In an example in Figure 3 17 there are 10 samples that have been added to the project but attributes have not yet been assigned To use the sample annotation file prepared in Figure 3 16 click Assign sample attributes from a file in the Data tab In the following file browser indicate if the text file is stored in My computer If so locate the file and then click Next Chapter 3 Creating and Analyzing a Project 18 Figure 3 17 Assigning attributes of samples using a sample annotation text file The first column of the table can contain either File names or Sample names and should be selected using the r
19. ng the dropdown box To delete a collaborator select the username and click the Delete selected collaborator button Figure 3 36 Collaborators tab controls the user accounts that are permitted to work in the current project Chapter 3 Creating and Analyzing a Project 35 3 7 Project management A project may be renamed or deleted using the Project actions button on the upper right side of the Project View page Figure 3 37 When deleting a project the user is given the choice to delete the output files of the project as well Figure 3 37 Project actions buttons highlighted allow renaming or deleting a project The user can also manage several projects all at once From the Partek Flow Home Page the user can see projects that have recent activity Clicking the link for View all projects will open the Project management page Figure 3 38 Figure 3 38 Accessing the project management page The Project management page lists all the projects accessible to the current use and the table shows the name owner and time of last activity for each project Clicking a Project name will go to the Project View of the selected project The list can be sorted according to a specific column using the sort icon Projects can be renamed or deleted Additional New projects can also be created from this page
20. pected to generate data nodes expected nodes appear even before the task is completed They will have a lighter shade of color to indicate that they have not yet been generated as the task is still being performed Once all tasks are done all nodes would appear in the same shade of blue such as in Figure 3 23 Chapter 3 Creating and Analyzing a Project 25 Figure 3 25 A running task showing the progress indicator the color darkens from left to right The expected output data node also in the lighter shade of color appears even before the task completes thus enabling the user to launch additional tasks while the computation is still in progress 3 4 3 Canceling and deleting tasks Tasks can only be cancelled or deleted by the user that started the task Running or pending tasks can be canceled by clicking the right mouse button on the task node and then selecting Cancel Figure 3 26 Alternatively the task node may be selected and the Cancel task selected from the task pane Chapter 3 Creating and Analyzing a Project 26 Figure 3 26 Canceling a task may be done by right clicking on the running task or by selecting Cancel task in the task panel Cancelled or failed tasks are flagged by small red circles with exclamation points on the tasks nodes Data nodes connected to incomplete tasks are also incomplete as no output can be generated Figure 3 27 For failure due to errors see the Task details which will be discussed
21. r adding samples inset Automatically create samples from files This method adds samples by creating them simultaneously as the data gets imported into a project The Sample names are assigned automatically based on the filenames Before proceeding it is ideal that you have already copied the data you wish to analyze in a folder with appropriate permissions within the Partek Flow server Please seek assistance from your system administrator in uploading your data directly Select the Automatically create samples from files button The next screen will feature a file browser that will show any folders you have access to in the Partek Flow server Figure 3 3 Select a folder by clicking the folder name Files in the Chapter 3 Creating and Analyzing a Project 4 selected folder that have file formats that can be imported by Partek Flow will be displayed and tick marked on the right panel Figure 3 3 You can exclude some files from the folder by unselecting the checkmark on the left side of the filename When you have made your selections click the Create samples button Figure 3 3 Selecting files in the Partek Flow server to be imported in a project Alternatively files can also be uploaded and imported into the project from the user s local computer Select the My computer radio button Figure 3 4 and the options of selecting the local file and the upload destination directory will appear Only one file at a time can be impo
22. rted to a project using this method Figure 3 4 Selecting files from the user s local computer for upload and import Multiple data files can be compressed a single zip file before uploading Partek Flow will automatically unzip the files and put them in the upload directory Please be aware that the use of the method illustrated in Figure 3 4 highly depends on the speed and latency of the Internet connection between the user s computer and the server where Partek Flow is installed It is not recommended in most cases Chapter 3 Creating and Analyzing a Project 5 After successful creation of samples from files the Data tab now contains a sample management table Figure 3 5 The Sample name column in the table is automatically generated based on the filenames and the table is sorted in alphabetical order Clicking the expand triangle on the right side of the sample management table will expand the table and reveal the filename of the files associated with each sample Figure 3 5 inset Similarly the collapse triangle will hide the file information The fastq column in the expanded view shows the filename associated with the sample Any filename extensions that indicate compression such as gz are not shown Figure 3 5 Data tab containing the sample management table after samples were added successfully Inset shows the expanded view Once a sample is created in a project the files associated with it can be modi
23. samples can be added Information such as disease type age treatment or sex can be annotated to the data by assigning the Attributes for each sample Certain tasks in Partek Flow such as Gene Specific Analysis require that samples be assigned attributes in order to do statistical comparison between groups or samples As attributes are added to the project additional columns in the sample management table will be created Sample attributes Attributes can be managed or created within a project Under the Data tab click the button to open the Manage attributes page Figure 3 9 Chapter 3 Creating and Analyzing a Project 10 Figure 3 9 Accessing the Manage attributes page from the Data tab To prepare for later data analysis using statistical tools attributes can be categorical or numeric i e continuous Adding a categorical attribute For categorical attributes there are two levels of visibility Project specific categorical attributes are visible only within the current project System wide categorical attributes are visible in all the projects within the Partek Flow instance and are useful for maintaining uniformity of terms throughout the Flow installation Importing samples in a new project will retain the system wide but not the project specific attributes Only users of the Partek Flow server who have been given administrative privileges can create System wide categorical attributes See section on User management of C
24. signed a value To edit the table click Edit sample attributes Assign the sample attributes by using a drop down for categorical attributes controlled vocabulary or typing with a keyboard for numeric attributes Figure 3 14 inset Chapter 3 Creating and Analyzing a Project 15 Figure 3 14 A blank sample management table showing attribute columns The samples have to be categorized or assigned a value inset an example is shown When all the attributes have been given a value click Apply changes and the sample management table will be updated An example of a completed sample management table is shown in Figure 3 15 After editing the sample table make sure there are no fields with blank or N A values before proceeding To rename or delete attributes click Manage attributes from the Data tab to access the Manage attributes page Figure 3 9 You cannot delete an attribute if a sample is assigned to it Chapter 3 Creating and Analyzing a Project 16 Figure 3 15 Sample management table with sample attributes assigned an example is shown Chapter 3 Creating and Analyzing a Project 17 Assigning attributes using a Sample Annotation Text File Another way to assign attributes to samples in the Data tab is to use a text file that contains the table of attributes and categories values This table is prepared outside of Partek Flow using a text editing software capable of saving tab separated text files Usi
25. stem wide They can also restrict the modification of a Project specific attribute exclusively to other admin accounts Chapter 3 Creating and Analyzing a Project 12 An additional feature to facilitate the controlled vocabulary in Partek Flow is the integration of terms used by SNOMED CT a healthcare terminology used for electronic health records They can be added easily by managing the categories of an attribute and selecting Import terms from SNOMED CT shown in Figure 3 11 Available terms include those for body structure specimen clinical findings or organism Select multiple terms from SNOMED CT by holding Ctrl key on the keyboard while clicking the mouse to select These terms will become new top level categories in your attribute When terms are imported from SNOMED CT the Term depth indicates the number of sublevels that will also be imported as subcategories in your attribute Figure 3 11 Importing SNOMED CT terms as categories Adding a numeric attribute To add a categorical attribute in the Manage attributes page click the Add new attribute Figure 3 12 In the dialog box type a Name for the attribute select the Numeric radio button next to Attribute type and then click the Add button Some optional parameters for numeric attributes include the Minimum value Maximum value and Units When done click Add to return to the Manage attributes page Repeat the process add more numeric attributes When done click Back to sampl
26. y to a transcriptome task report is shown as an example Chapter 3 Creating and Analyzing a Project 29 The Task details shows detailed diagnostic information about the task Figure 3 31 It includes the duration and parameters of the task lists of input and output files and the actual commands in the command line that were run Figure 3 31 An example of Task details page A Quantify to a transcriptome task report is shown as an example Additionally the Task details page would be where the error logs of unsuccessful runs similar to the one shown in Figure 3 27 may be obtained The user can download the logs or send them to Partek This page plays an important role in diagnosing and troubleshooting issues related to task Double clicking on a task node will show the Task report page However if no report was generated the user will be directed to the Task details page In the Task actions sections the selected task can be Re run w new parameters and in case it is part of a pipeline that includes additional tasks after it running the Downstream tasks is an option Re running tasks will result in Layers and will be described in the following section Chapter 3 Creating and Analyzing a Project 30 Another action available for a task node is Add task description Figure 3 32 which is a way to add notes to the project The user can enter a description which will be displayed when the mouse pointer is hovered over the task node
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